Adjust run configuration in a plugin

I'm writing a PyCharm plugin, and I want it to run a modified version of the selected run configuration. How can I clone the selected run configuration, modify it, and then launch a process? I also want to be able to send a string to the process's stdin and read the process's stdout. I don't want the process to be displayed in the usual console, because I'm going to display the stdout text in my plugin.

I found this post about creating a new run configuration, but I don't know how to access the stdin and stdout. Also, when I tried to clone an existing run configuration, my changes affected the original.